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Almond Flour Lemon Poppy Seed Muffins (Gluten Free, Paleo)

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Almond Flour Lemon Poppy Seed Muffins – These gluten-free lemon poppy seed muffins have a light, fluffy texture and are BURSTING with lemon flavor. They’re the perfect yummy breakfast or snack! (Gluten-Free + Paleo)

Gluten Free & Paleo Almond Flour Lemon Poppy Seed Muffins from One Lovely Life

We live in one of the sunniest states in the U.S., so we have VERY mild winters, but I always find that March feels like turning an energizing corner from winter to spring. In the kitchen, this means I only have a little longer to wait before berries are in season (my kids can’t WAIT), and we have the last of winter’s sunny citrus to send us off.

Lemon always tastes like sunshine to me, which is why just about every spring I get the itch to make something lemony! I’ve posted plenty of lemon things on this blog from soup to salad to cake, and today I’ve got a lemony breakfast that feels perfect for spring (or Easter brunch down the road): Almond Flour Lemon Poppy Seed Muffins!

Packed with LOTS of lemon flavor and dotted with poppy seeds, these light, tender muffins are made from better-for-you ingredients and taste incredible. Like, IN👏CRE👏DI👏BLE👏.

Preheat the oven and bust out the muffin pan! Here’s all you need to get started:

Gluten Free & Paleo Almond Flour Lemon Poppy Seed Muffins from One Lovely Life
Gluten Free & Paleo Almond Flour Lemon Poppy Seed Muffins from One Lovely Life


  • LEMON ZEST + LEMON JUICE. To start off, these lemon poppy seed muffins get a super-charged dose of lemon flavor with a combination of fresh lemon zest and lemon juice. I love the brightness of fresh lemons!
  • AVOCADO OIL + EGGS + (DAIRY FREE) MILK. Typical muffin ingredients. I like avocao oil because it’s so neutral-tasting, but you can substitute another, if you like. We’re dairy-free, so I use a dairy-free milk like almond, cashew, etc. You can use whatever your family drinks! The milk will also take on some acidity from the lemon juice, which adds a buttermilk effect here. The result is extra light, fluffy, tender muffins. Win-win!
  • MAPLE SYRUP OR HONEY. To keep these muffins naturally sweetened, I love using pure maple syrup or some good-quality honey. Both allow the lemon flavor to really shine!
  • VANILLA + LEMON EXTRACT (OPTIONAL). Vanilla adds another layer of sweetness and tastes lovely with the lemon. If you like your lemon muffins extra punchy (like I do!), I recommend adding the optional lemon extract. (You can also use 1 drop food grade lemon essential oil)
  • ALMOND FLOUR. You’re looking for finely ground blanched almond flour. The finer, the better! Almond flour is pretty moist and a little dense on its own, so I pair it with…
  • TAPIOCA STARCH OR ARROWROOT. You can use either of these starchy flours that keep the muffins light and fluffy and give them their soft, delicate crumb. I don’t recommend skipping it or substituting it with more almond flour, or your muffins will not rise and hold together as well. (Don’t have either of these? Cornstarch is your best substitute.)
  • BAKING POWDER + BAKING SODA + SALT. The baking powder and soda give these gluten free lemon poppy seed muffins their lovely rise, keep them tender, and neutralize the acidity of the lemon juice. Then, salt helps balance the flavors. (Paleo? See the FAQ below!)
  • POPPY SEEDS. Poppy seeds won’t really add much flavor-wise, but they’re a pretty addition to the muffins and give them their signature look. I get mine in the spices section of the grocery store.
Gluten Free & Paleo Almond Flour Lemon Poppy Seed Muffins from One Lovely Life
Gluten Free & Paleo Almond Flour Lemon Poppy Seed Muffins from One Lovely Life


Making a brunch out of it? Here are some of our favorite things to pair with these almond flour lemon poppy seed muffins:

Gluten Free & Paleo Almond Flour Lemon Poppy Seed Muffins from One Lovely Life
Gluten Free & Paleo Almond Flour Lemon Poppy Seed Muffins from One Lovely Life


CAN I USE ANOTHER FLOUR? Probably not, I’m sorry! I don’t recommend swapping in coconut flour or omitting the tapioca starch or arrowroot. This gluten-free lemon poppyseed muffins recipe was tested based on the moisture of the almond flour (which is different than white flour or gluten-free flour blends). The one exception is you *can* use cornstarch in place of the arrowroot or tapioca starch.

WHAT’S THE BEST WAY TO STORE LEFTOVER MUFFINS? I store leftover lemon poppy seed muffins in a bag on the counter for 1-2 days, or in the refrigerator for 2-3. They’ll also keep up to a couple of months in the freezer!

PALEO? READ THIS. These can absolutely be made as paleo lemon poppy seed muffins, as almost every ingredient is paleo-approved. If you’re strictly paleo, you’ll want to substitute a paleo baking powder option and skip the optional dusting of turbinado sugar. All the other ingredients are A-ok!

THE BEST MUFFIN PANS & MUFFIN CUPS. For perfectly non-stick lemon poppy seed muffins, I recommend using parchment liners like these in a metal muffin pan. You’ll get golden edges and the wrappers come right off. If you don’t want to fuss with liners, we love using a silicone muffin pan like this. They’re great and naturally nonstick!



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Gluten Free & Paleo Almond Flour Lemon Poppy Seed Muffins from One Lovely Life

Almond Flour Lemon Poppy Seed Muffins (Gluten Free, Paleo)

5 Stars 4 Stars 3 Stars 2 Stars 1 Star

5 from 6 reviews

  • Author: One Lovely Life
  • Total Time: 25 minutes
  • Yield: 12 Muffins 1x


Almond Flour Lemon Poppy Seed Muffins – These gluten-free lemon poppy seed muffins have a light, fluffy texture and are BURSTING with lemon flavor. They’re the perfect yummy breakfast or snack!



Wet Ingredients:

  • 2 Tbsp. fresh lemon zest (from about 2 lemons)
  • 2 Tbsp. fresh lemon juice (about 1 lemon)
  • 1/3 cup milk* (I use unsweetened almond milk)
  • 1/3 cup pure maple syrup or honey
  • 1/4 cup avocado oil
  • 3 eggs
  • 1 tsp. vanilla extract
  • 1/2 tsp. lemon extract (optional)

For the Dry Ingredients:

  • 2 1/2 cups blanched almond flour (finely ground)
  • 1/2 cup tapioca starch or arrowroot*
  • 1 tsp. baking powder
  • 1/2 tsp. baking soda
  • 1/4 tsp. salt
  • 2 Tbsp. poppy seeds

Optional: 2-3 tsp. turbinado sugar for decoration.


  1. Preheat the oven to 350 degrees F. Grease a muffin pan or line with parchment muffin liners.
  2. In a large bowl, combine the wet ingredients. Stir together lemon zest, lemon juice, milk, syrup, oil, eggs, vanilla, and lemon extract (if using). Whisk until smooth.
  3. Next, add the dry ingredients. Add almond flour, tapioca starch, baking powder, baking soda, salt, and poppy seeds to the wet ingredients. Stir until just combined.
  4. Scoop or spoon batter into prepared muffin pan.
  5. If desired, sprinkle the tops of the muffins with turbinado sugar.
  6. Bake muffins at 350 degrees F. for 15-18 minutes, or until slightly golden and a toothpick inserted in the center comes out clean with just a few moist crumbs.
  7. Allow muffins to cool 1 minute in the muffin pan before transferring to a cooling rack.


*You can use any kind of milk for this recipe–dairy or non-dairy. Whatever you drink! If you don’t have/can’t find tapioca starch or arrowroot, you can substitute cornstarch.

  • Prep Time: 10 minutes
  • Cook Time: 15-18 minutes
  • Category: Breakfast, Muffins
  • Method: Baking
  • Cuisine: American

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  1. Delicious! Awesome lemon flavor and great moist texture. Kids and I made them to surprise my dairy-free / gluten-free wife this morning (Mother’s Day). We didn’t have poppy seeds so I added blueberries to half and chopped blackberries to other half. These muffins were a big hit. Thank you!! Will make them again soon.

  2. Currently waiting for them to come out of the oven… This quarantine has me eating so poorly lately… Trying to get back on track with a paleo-esque mostly grain/dairy free diet… I made a few substitutions I want to note in case they still come out good and it’s all someone else has on hand like me. I used chia seeds instead of poppy seeds, I used half almond flour and half sunflower seed flour, cornstarch instead of arrowroot or tapioca, 2 teaspoons dried zest instead of fresh,and coconut sugar syrup instead of honey or maple. they are dark I can tell so far, most likely due to the sunflower seeds and the coconut syrup.. we’ll see fingers crossed 😀 … Had enough batter for the 12 muffins and a tray of 24 minis, think I may have used to much sunflower seed flour, as I made it just for this and may have used a tad too many seeds… Oh well, the timers beeping…

    I’ve used sunflower seed flour in the past to make chocolate chip cookies and after about a day i think it was baking soda or baking powder but it reacts and they turned green.. it was super cool, I kinda hope it happens with these as well..

    OK ate a few mini ones, as they finished first… Pretty good, especially with butter.. I didn’t use the lemon extract so the lemon flavor is weak, but that’s ok for me… honestly they remind me kind of like cornbread muffins a little more than lemon poppy seed muffins, but I suspect that is mostly, if not entirely, to do with the consistency in which I ground my sunflower seed flour… Would be much better with %100 fine almond flour. I’d say chia seeds make a pretty good sub for poppy seeds as well…

  3. I’m wondering what the best way to convert this recipe to almond poppyseed muffins might be? If I leave out the lemon juice what I need to increase the amount of almond milk? Of course I would add almond extract instead of lemon extract. Any thoughts or suggestions?

  4. THANK YOU for such a fabulous recipe, I just finished baking and eating one, and I am flawed by the lightness, moistness, and subtle sweetness of these muffins. They are wonderful. Thankfully, there are eleven more to enjoy! x

  5. I’ve been struggling finding gf baking that satisfies my needs. I’ve tried few a gf recipes and they didn’t live up to the test. But this one does! So delicious !!! They rose well, didn’t fall apart, were moist and tasted sooooooooo good! Thank you for changing my mind that gf baking can be easy, and delicious!

  6. Delicious texture. Could have been a tad bit sweeter for me, and a bit more lemony. Otherwise, so soft and moist, crisp on the edges, and so fluffy. Thanks 🙂

    1. Can you use any other oil besides avocado oil? Which is better to use Arrowroot or tapioca starch? I would like to be able to use whatever I get in other recipes.

      1. You can substitute another neutral-tasting oil (like grapeseed, canola, etc.) in place of the avocado oil. Arrowroot and tapioca starch will both work equally well in this recipe. I think you’d be more likely to see arrowroot in other recipes, so if you’re going to invest in one, that’s one I’d recommend!

        You can also use arrowroot in our Almond Flour Chocolate Zucchini Cake!

  7. I made these yesterday. I made several changes though. We were out of lemon so I used fresh orange juice from a small orange and a large orange. I added vanilla, increased the honey by 1/4 cup and folded in a cup of coconut. Next time I would toast the coconut, but, they were delicious.

    1. I wouldn’t, since chia seeds will absorb liquid from the batter, which could make your muffins turn out try. I’d just omit the seeds altogether if you don’t have/like poppy seeds 🙂

  8. These are by far the most light, fluffy, and delicious almond flour muffins that I have ever made. The recipe is beautiful as written. I also have made it with a mix of lemon and orange juice and zest, and that was outstanding as well. I found that 1/4 c sweetener is plenty; I just added an extra Tablespoon of juice to keep the liquid balance.
    Thank you for this gift of a recipe!

  9. I just found this found this recipe and it sounded great cholesterol wise but was very surprised at the 46.5mg amount. Could you let me know what ingredient is doing that? Thanks!

    1. Anne – That’ll be the eggs! I don’t recommend egg substitutes here since they’re crucial for the structure of the muffins. (Almond flour is a bit more finicky)

  10. I made some changes because of my high cholesterol but this recipe allowed for these adjustments perfectly.
    Instead of 2.5 cups almond flour I did 1 cup and 1.5 cups oat flour. Used only 2 eggs. Added 1/2 cup of frozen wild blueberries. Thank you!

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